DAVIDResult-class: class "DAVIDResult

In RDAVIDWebService: An R Package for retrieving data from DAVID into R objects using Web Services API.

Description

This class represents the most generic result obtained in the Database for Annotation, Visualization and Integrated Discovery (DAVID) website (see References).

Type

This class is a "Virtual" one.

Heirs

• DAVIDGenes: basic gene information (ID, Name and Specie)

• DAVIDCluster: generic Cluster result (Term or Gene).

• DAVIDFunctionalAnnotationChart: EASE results on each Functional Category (see references).

• DAVIDFunctionalAnnotationTable: annotation for each gene, no statistical analysis.

Slots

type

Object of class "character". Contains the name of DAVID's result.

Methods

show

signature(object="DAVIDResult"): returns a basic console output.

type

signature(object="DAVIDResult"): getter for type slot.

plot2D

signature(object="DAVIDResult", dataFrame="data.frame"): internal ggplot tile plot for gene/term cluster and annotation heirs.

Author(s)

Cristobal Fresno and Elmer A Fernandez

References

1. The Database for Annotation, Visualization and Integrated Discovery (david.abcc.ncifcrf.gov)

2. Huang, D. W.; Sherman, B. T.; Tan, Q.; Kir, J.; Liu, D.; Bryant, D.; Guo, Y.; Stephens, R.; Baseler, M. W.; Lane, H. C. & Lempicki, R. A. DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Res, Laboratory of Immunopathogenesis and Bioinformatics, SAIC-Frederick, Inc., National Cancer Institute at Frederick, MD 21702, USA., 2007, 35, W169-W175

3. Huang, D. W.; Sherman, B. T. & Lempicki, R. A. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res, Laboratory of Immunopathogenesis and Bioinformatics, Clinical Services Program, SAIC-Frederick, Inc., National Cancer Institute at Frederick, Frede#rick, MD 21702, USA., 2009, 37, 1-13

4. Xiaoli Jiao, Brad T. Sherman, Da Wei Huang, Robert Stephens, Michael W. Baseler, H. Clifford Lane, Richard A. Lempicki, DAVID-WS: A Stateful Web Service to Facilitate Gene/Protein List Analysis Bioinformatics 2012 doi:10.1093/bioinformatics/bts251

See Also

Other DAVIDResult: plot2D, plot2D, plot2D, plot2D, plot2D, plot2D, type, type

RDAVIDWebService documentation built on Nov. 8, 2020, 8:05 p.m.